Emission of methane and other trace gases from the Amazon Varzea

Researchers measured the distributions and fluxes of methane and other trace gases from the various Amazon floodplain environments. These were determined during both a large scale, quasi-synoptic survey along a 2000 km reach of the Amazon river and an intensive local study (by J. Melack, R. Harriss et al.) covering a six-week period. The environments studied included the major rivers, connecting channels (paranas), floating macrophyte beds, flooded forests, open lakes and recently wetted soils. The results are summarized. Measured rates of methane emission averaged about 300 mg m-2 d-1, but with considerable variance, and were comparable to or higher than previously reported emissions from similar temperature zone environments. In general, areas covered by floating macrophytes showed the highest emissions. Individual hotspots had among the highest rates ever observed, over 10 g m-2 d-1. The high methane emissions appear to result because about 50% of the organic matter fixed on the floodplain (either terrestrial or aquatic) that is oxidized in the water is decomposed anaerobically via methanogensis. Measured fluxes of methane to the atmosphere appear to be significantly correlated with surface water dissolved methane concentrations

Benthic fluxes and nitrogen cycling in sediments of the continental margin of the eastern North Pacific

The exchange of O2, N2, NO3−, NH4+, Si(OH)4, and PO4−3 between the sediments and the overlying water (benthic flux) was determined at 18 locations on the Washington State continental margin using an in situ benthic tripod. Oxygen consumption by the sediments ranged from 21.2 pmole cm−2 s−1 on the shelf to 2.85 pmole cm−2 s−1 on the slope. Nitrogen gas fluxes were from the sediments to the overlying water. They varied 5.5 to 1.2 pmole-N cm−2 s−1 and were always greater than the corresponding NO3− flux into the sediments. A nitrogen mass balance indicated that the difference between the N2 flux out and the NO3− flux in could be accounted for by oxidation of NH4+ produced during aerobic and anaerobic carbon remineralization to NO3− and subsequent denitrification to N2. Comparison of the benthic fluxes of O2, NO3− and Si(OH)4 with the fluxes predicted from molecular diffusion across the sediment water interface showed that for all three solutes the benthic fluxes were up to three times greater than the molecular fluxes and indicated the importance of macrobenthic irrigation in these sediments. However, several existing empirical irrigation models were not able to describe all three solutes. The overall carbon oxidation rate, as estimated from the sum of the O2 flux, the N2 flux and the measured SO4= reduction rate, could be fit with a normalized power function; i.e., carbon oxidation rate (gC m−2 y−1) = 110 · (z/100)−0.91. The exponent describing the rate of attenuation with depth (−0.91) was similar to the carbon rain rate attenuation coefficient determined from sediment traps in the pelagic, eastern North Pacific

Simultaneous nitrate and oxygen respiration in coastal sediments: Evidence for discrete diagenesis

Oxygen and nitrate porewater profiles from sediments of Puget Sound, the Washington continental margin, and the Chukchi Sea were determined using a whole core squeezing apparatus. The two oxidants were observed to have equal sediment penetration depths and similar profile shapes in nearly all cores. Oxygen and nitrate, therefore, behaved in a similar manner in these shallow sediments: an observation that is not consistent with existing models of sediment diagenesis. A two-dimensional model was constructed in which nearly all oxidant (O2 and NO3−)consumption took place in scattered, highly reactive discrete micro-sites. The model produced a sedimentary environment in which reactions at each micro-site were limited by oxidant concentrations with oxidant gradients extending well beyond the micro-sites into relatively nonreactive bulk sediments. Thus for a given depth surface within the sediment, oxygen concentrations were much lower at micro-sites than average concentrations on that surface. Furthermore, at most micro-sites oxygen concentrations were sufficiently low enough to permit simultaneous denitrification, which explained the apparent similarity between oxygen and nitrate concentration profiles within these sediments. The model suggests that a relatively few, short-lived reaction sites are responsible for most oxygen and nitrogen reduction within oxic sediments under shallow seas, and it is consistent with emerging concepts about the fate of organic carbon in coastal sediments

Oxidation and reduction rates for organic carbon in the Amazon mainstream tributary and floodplain, inferred from distributions of dissolved gases

Concentrations of CO2, O2, CH4, and N2O in the Amazon River system reflect an oxidation-reduction sequence in combination with physical mixing between the floodplain and the mainstem. Concentrations of CO2 ranged from 150 microM in the Amazon mainstem to 200 to 300 microM in aerobic waters of the floodplain, and up to 1000 microM in oxygen-depleted environments. Apparent oxygen utilization (AOU) ranged from 80 to 250 microM. Methane was highly supersaturated, with concentrations ranging from 0.06 microM in the mainstem to 100 microM on the floodplain. Concentrations of N2O were slightly supersaturated in the mainstem, but were undersaturated on the floodplain. Fluxes calculated from these concentrations indicated decomposition of 1600 g C sq m y(-1) of organic carbon in Amazon floodplain waters. Analysis of relationships between CH4, O2, and CO2 concentrations indicated that approximately 50 percent of carbon mineralization on the floodplain is anaerobic, with 20 percent lost to the atmoshphere as CH4. The predominance of anaerobic metabolism leads to consumption of N2O on the flood plane. Elevated concentrations of CH4 in the mainstem probably reflect imput from the floodplain, while high levels of CO2 in the mainstem are derived from a combination of varzea drainage and in situ respiration

Metal Reduction at Cold Temperatures by Shewanella Isolates from Various Marine Environments

Members of the genus Shewanella capable of reducing metals and forming minerals under cold-temperature conditions were isolated from 3 distinct marine habitats (the coast of Wash- ington State, the Puget Sound, and an iron-rich microbial mat off Hawaii). Cultures of microorgan- isms were isolated at 8°C on nutrient agar medium prepared in artificial seawater. Isolates in this study could use a wide variety of electron acceptors such as oxygen, nitrate, and metals, and reduce various metals coupled to the oxidation of several organic acids, glucose or hydrogen at temperatures down to 0°C. Akaganeite was reduced to either magnetite or siderite, depending on the test condi- tions. The geochemical profiles at the sample sites from which these strains were isolated spanned a temperature range of 1.8 to 11°C, and all showed active oxygen and nitrate reduction as well as metal reduction. This confirms previous reports that sediment microorganisms participating in biogeo- chemical cycles remain active at low temperatures

Nutrient and Phytoplankton Dynamics on the Inner Shelf of the Eastern Bering Sea

In the Bering Sea, the nitrogen cycle near Nunivak Island is complicated due to limited nutrient replenishment across this broad shelf, and substantial nitrogen loss through sedimentary processes. While diffusion at the inner front may periodically support new production, the inner shelf in this region is generally described as a regenerative system. This study combines hydrographic surveys with measurements of nitrogen assimilation and benthic fluxes to examine nitrogen cycling on the inner shelf, and connectivity between the middle and inner shelves of the southern and central Bering Sea. Results establish the inner shelf as primarily a regenerative system even in spring, although new production can occur at the inner front. Results also identify key processes that influence nutrient supply to the inner shelf and reveal coupling between the middle shelf nutrient pool and production on the inner shelf

Benthic oxygen consumption rates during hypoxic conditions on the Oregon continental shelf: Evaluation of the eddy correlation method

Three stations, at ∼80 m water depth on the Oregon shelf between 44.7°N and 43.9 N, were studied under hypoxic conditions in late spring and summer of 2009 to determine benthic oxygen consumption rates. Oxygen fluxes were derived from eddy correlation (EC) measurements made from an autonomous lander deployed for 11–15 h at a time. Average oxygen consumption rates ranged from 3.2 to 9.8 mmol m⁻² d⁻¹ and were highest at the southernmost station. Methods for separating eddy components and rotating coordinates were examined for effects on EC fluxes. It was found that oscillations at frequencies associated with surface and internal waves made significant contributions, but horizontal component biasing could be minimized by wave-based rotation methods. Additional measurements included benthic boundary layer properties, and sediment permeability and profiles of sediment organic C, chlorophyll-a, excess ²¹⁰Pb and % fines. Comparative flux estimates were determined from benthic chamber measurements and microelectrode profiles at two of the stations. The chamber O₂ consumption rates exceeded the EC fluxes by factors of 1.2–1.8, which may reflect enclosure effects, the different spatial and temporal scales of the measurements, and/or inhomogeneous benthic respiration rates. The magnitudes of the fluxes by either method, however, are low for shelf depths. Thus, for benthic O₂ consumption to contribute to Oregon shelf hypoxia, bottom waters must be slowly renewed and minimally ventilated by along- or across-shelf advection and turbulent mixing. Circulation studies indicate these conditions are favored by increased near-bottom stratification during persistent summer upwelling- relaxation cycles

Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota

Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1^T, HCA1^T, HCE1^T and PS0^T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15–0.26 µm in diameter and 0.50–1.59 µm in length. Motility was not observed, although strain PS0^T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1^T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76^T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1^T, HCE1^T, and PS0^T. Strain PS0^T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B_1 (thiamine), B_2 (riboflavin), B_6 (pyridoxine), and B_(12) (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0–34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76^T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1^T (=ATCC TSD-97^T =NCIMB 15022^T), HCA1^T (=ATCC TSD-96^T), HCE1^T(=ATCC TSD-98^T), and PS0^T (=ATCC TSD-99^T) are type strains of the species Nitrosopumilus maritimus sp. nov., Nitrosopumilus cobalaminigenessp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria